Hattie Chung, PhD
Cards
Research
About
Research
About
Research
Hattie Chung Lab
Titles
Assistant Professor
Education
Harvard University, Systems Biology (2016)
Massachusetts Institute of Technology, Biological Engineering (2011)
Appointments
Titles
Assistant Professor
Education
Harvard University, Systems Biology (2016)
Massachusetts Institute of Technology, Biological Engineering (2011)
Appointments
Titles
Assistant Professor
Education
Harvard University, Systems Biology (2016)
Massachusetts Institute of Technology, Biological Engineering (2011)
Appointments
Hattie Chung Lab
Titles
Assistant Professor
Education
Harvard University, Systems Biology (2016)
Massachusetts Institute of Technology, Biological Engineering (2011)
Appointments
Titles
Assistant Professor
Education
Harvard University, Systems Biology (2016)
Massachusetts Institute of Technology, Biological Engineering (2011)
Appointments
Titles
Assistant Professor
Education
Harvard University, Systems Biology (2016)
Massachusetts Institute of Technology, Biological Engineering (2011)
Appointments
Hattie Chung Lab
About
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Titles
Assistant Professor
Biography
Dr. Hattie Chung is an Assistant Professor of Medicine (Cardiology) and of Molecular, Cellular and Developmental Biology, and a member of the Cardiovascular Research Center. She is a systems and computational biologist with a strong track record of designing cutting-edge methods for obtaining and analyzing high-dimensional genomic data, applied to uncover the cellular organization of tissues. Her lab studies the molecular basis of cellular heterogeneity and tissue organization in health and disease by pioneering computational and experimental methods, with an emphasis on single-cell and spatial genomics technologies. She leads an interdisciplinary team that focuses on ovarian aging, cardiovascular disease, and predictive modeling of drug perturbations.
Dr. Chung completed her PhD in Systems Biology at Harvard University, where she studied evolutionary dynamics during infections using computational genomics, and her BS in Biological Engineering at the Massachusetts Institute of Technology, where she studied synthetic biology and drug delivery. As a postdoc at the Broad Institute of MIT and Harvard, she developed single-cell methods that have been widely recognized.
Lab: www.hattiechunglab.bio
Appointments
Cardiovascular Medicine
Assistant ProfessorPrimary
Other Departments & Organizations
- Cardiovascular Medicine
- Center for RNA Science and Medicine
- Computational Biology and Biomedical Informatics
- Internal Medicine
- Molecular Cell Biology, Genetics and Development
- Molecular Medicine, Pharmacology, and Physiology
- Vascular Biology and Therapeutics Program
- Yale Cardiovascular Research Center (YCVRC)
- Yale Center for Research on Aging (Y-Age)
- Yale Center for Systems and Engineering Immunology (CSEI)
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
Education & Training
- Postdoctoral Associate
- The Broad Institute of MIT and Harvard (2024)
- PhD
- Harvard University, Systems Biology (2016)
- BS
- Massachusetts Institute of Technology, Biological Engineering (2011)
Research
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Overview
Public Health Interests
ORCID
0000-0001-8417-5606- View Lab Website
Hattie Chung Lab
Publications
2024
Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation
Tamura T, Cheng C, Villaseñor-Altamirano A, Yamada K, Ikeda K, Hayashida K, Menon J, Chen X, Chung H, Varon J, Chen J, Choi J, Cullen A, Guo J, Lin X, Olenchock B, Pinilla-Vera M, Manandhar R, Sheikh M, Hou P, Lawler P, Oldham W, Seethala R, Baron R, Bohula E, Morrow D, Blumberg R, Chen F, Merriam L, Weissman A, Brenner M, Chen X, Ichinose F, Kim E, Sohn H, Rolland T, Weil B. Diverse NKT cells regulate early inflammation and neurological outcomes after cardiac arrest and resuscitation. Science Translational Medicine 2024, 16: eadq5796. PMID: 39630883, PMCID: PMC11792709, DOI: 10.1126/scitranslmed.adq5796.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsOut-of-hospital cardiac arrestCohort of patientsNeurological outcomeT cellsImmune cellsCardiac arrestNatural killer (NK) cellsAssociated with good neurological outcomesDiverse T cell receptor repertoireNeurological injuryT cell receptor repertoireAssociated with poor neurological outcomeIncreased inflammatory chemokineInnate T cellsPoor neurological outcomeWild-type micePost-cardiac arrestAccumulation of macrophagesIncreased neuronal injuryBrains of miceNKT cellsTreated miceReceptor repertoireInflammatory chemokinesCytokine expression
2022
Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections
Chung H, Merakou C, Schaefers M, Flett K, Martini S, Lu R, Blumenthal J, Webster S, Cross A, Al Ahmar R, Halpin E, Anderson M, Moore N, Snesrud E, Yu H, Goldberg J, O’Toole G, McGann P, Stam J, Hinkle M, McAdam A, Kishony R, Priebe G. Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections. Nature Communications 2022, 13: 1231. PMID: 35264582, PMCID: PMC8907320, DOI: 10.1038/s41467-022-28188-w.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAntibiotic resistance mutationsResistance mutationsLong-read sequencingEvolution of antibiotic resistanceSputum samplesRespiratory infectionsCulture-based methodsLow-frequency resistance mutationsColonization bottlenecksEarly stages of infectionDays of therapyAcute bacterial infectionBacterial respiratory infectionsMechanically Ventilated PatientsGenomic surveillanceResistance phenotypeStages of infectionAntibiotic resistanceIn vivo frequencyAntibiotic therapyAntibiotic changeMutationsAntibiotic switchTherapy choiceIndividual patients
2021
Joint single-cell measurements of nuclear proteins and RNA in vivo
Chung H, Parkhurst C, Magee E, Phillips D, Habibi E, Chen F, Yeung B, Waldman J, Artis D, Regev A. Joint single-cell measurements of nuclear proteins and RNA in vivo. Nature Methods 2021, 18: 1204-1212. PMID: 34608310, PMCID: PMC8532076, DOI: 10.1038/s41592-021-01278-1.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGene expressionNuclear proteinsAnalysis of transcription factor (TFTranscription factor (TFGenome-wide associationRNA in vivoQuantitate protein levelsNative tissue contextModel gene expressionGene expression in vivoGene networksExpression in vivoInduction of neuronal activityGene targetingClinical specimensTissue contextGenesTranscriptomeProtein levelsProteinMouse brainExpressionCellular indicesPharmacological inductionTF
2019
The microbiota regulate neuronal function and fear extinction learning
Chu C, Murdock M, Jing D, Won T, Chung H, Kressel A, Tsaava T, Addorisio M, Putzel G, Zhou L, Bessman N, Yang R, Moriyama S, Parkhurst C, Li A, Meyer H, Teng F, Chavan S, Tracey K, Regev A, Schroeder F, Lee F, Liston C, Artis D. The microbiota regulate neuronal function and fear extinction learning. Nature 2019, 574: 543-548. PMID: 31645720, PMCID: PMC6818753, DOI: 10.1038/s41586-019-1644-y.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsMeSH KeywordsAnimalsAnti-Bacterial AgentsAutistic DisorderBloodCalciumCerebrospinal FluidCuesDendritic SpinesExtinction, PsychologicalFearFecesGerm-Free LifeIndicanMaleMetabolomicsMiceMice, Inbred BALB CMice, Inbred C57BLMicrobiotaNeural InhibitionNeurogliaNeuronsPhenylpropionatesPrefrontal CortexSchizophreniaTranscriptomeVagus NerveConceptsFear extinction learningMedial prefrontal cortexExtinction learningMicrobiota-derived signalsPrefrontal cortexNeuropsychiatric disordersAdult miceSusceptibility to neuropsychiatric disordersInfluence many physiological processesGerm-free adult miceTranscranial two-photon imagingMicrobiota-derived compoundsSingle-nucleus RNA sequencingGerm-free miceComplex consortiaMulticellular organismsPostsynaptic dendritic spinesBrain healthBrain functionRNA sequencingMicrobiotaIn adulthoodGene expressionNeuronal activityPostnatal neurodevelopment
2017
Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung
Chung H, Lieberman T, Vargas S, Flett K, McAdam A, Priebe G, Kishony R. Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung. Nature Communications 2017, 8: 14078. PMID: 28102223, PMCID: PMC5253648, DOI: 10.1038/ncomms14078.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPathogen Stenotrophomonas maltophiliaAdaptive mutationsGenetically close isolatesLocation‐specific selectionsDistant lineagesBacterial genesSpatial co-occurrenceBacterial populationsLocal selectionPathogensMutationsLineagesGenesCystic fibrosisGenomeGeneticsSubpopulationsSequencePhenotypeIsolatesHuman lung
2016
RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq
Kelsic E, Chung H, Cohen N, Park J, Wang H, Kishony R. RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Systems 2016, 3: 563-571.e6. PMID: 28009265, PMCID: PMC5234859, DOI: 10.1016/j.cels.2016.11.004.Peer-Reviewed Original ResearchCitationsAltmetricConceptsCodon choiceMAGE-seqRNA structureEnhanced translation initiationSynonymous codon choiceRNA folding predictionsDisruption of native structureSynthetic biology applicationsRNA structure determinationAmplicon deep sequencingGenes infACodon distributionCodon preferenceOptimal codonsTranslation initiationFold predictionRNA conformationDeep sequencingCodon optimizationCodonGene expressionCodon mutantsNative structureGenesMutants
2015
Isocost Lines Describe the Cellular Economy of Genetic Circuits
Gyorgy A, Jiménez J, Yazbek J, Huang H, Chung H, Weiss R, Del Vecchio D. Isocost Lines Describe the Cellular Economy of Genetic Circuits. Biophysical Journal 2015, 109: 639-646. PMID: 26244745, PMCID: PMC4572570, DOI: 10.1016/j.bpj.2015.06.034.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsGenetic circuitsRibosome binding site strengthsBinding site strengthsPlasmid copy numberProduction of proteinsInduced genesCellular economyCopy numberReporter genePlasmidLiving cellsGenesRegulatory pathProteinTranslation resourcesSite strengthProtein concentrationRibosomeLinesEffects of such couplingCellsInexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
Baym M, Kryazhimskiy S, Lieberman T, Chung H, Desai M, Kishony R. Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes. PLOS ONE 2015, 10: e0128036. PMID: 26000737, PMCID: PMC4441430, DOI: 10.1371/journal.pone.0128036.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsLibrary preparationCost of library preparationCost of sequencingWhole-genome sequencingMegabase-sizedGenomic libraryArtificial chromosomeRe-sequencingIllumina sequencingCustom barcodesGenetic screeningSequencing applicationsViral genomeRNA sequencingCost of sample preparationEvolution experimentsGenomeModern biologySequenceChromosomeCheaper equivalentsEnvironmental samplesInexpensive preparationNexteraHiSeq
2012
Lipid-derived nanoparticles for immunostimulatory RNA adjuvant delivery
Nguyen D, Mahon K, Chikh G, Kim P, Chung H, Vicari A, Love K, Goldberg M, Chen S, Krieg A, Chen J, Langer R, Anderson D. Lipid-derived nanoparticles for immunostimulatory RNA adjuvant delivery. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: e797-e803. PMID: 22421433, PMCID: PMC3325698, DOI: 10.1073/pnas.1121423109.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsToll-like receptorsSuppress influenza virus replicationVaccine adjuvantsActivation of Toll-like receptorsPeripheral blood mononuclear cellsHuman peripheral blood mononuclear cellsInfluenza virus replicationType I IFN activityBlood mononuclear cellsResponses in vitroAdaptive immune responsesCell-mediated responsesTLR-expressing cellsIn vivo therapyCell-specific deliveryToll-like receptor 8Adjuvant deliveryAntiviral immunotherapySystemic biodistributionImidazoquinoline familyTLR7-dependentTLR7/8 agonistMononuclear cellsSubcutaneous injectionImmune response
Teaching & Mentoring
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Teaching
Didactic MCDB 370: Biotechnology
LecturerLecture SettingDetails2/1/2024 - PresentForUndergraduate6 Average Instructional Hours Per YearThe principles and applications of cellular, molecular, and chemical techniques that advance biotechnology. The most recent tools and strategies used by industrial labs, academic research, and government agencies to adapt biological and chemical compounds as medical treatments, as industrial agents, or for the further study of biological systems.
Willing and Available to Mentor
- Postdoctoral Researchers
- Residents
- Clinical Fellows
- Students
News
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News
- June 17, 2026
Aging Reshapes the Ovary Long Before Reproductive Function Ends
- May 25, 2026
Understanding the Immune System to Predict, Prevent, and Treat Diseases
- November 03, 2025
Using Cutting Edge Basic Science Research To Address Real-World Questions
- April 17, 2025Source: Google Research
Teaching machines the language of biology: Scaling large language models for next-generation single-cell analysis
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Locations
300 George Street
Lab
New Haven, CT 06511